This is a bug in Waybar, which I suppose you are using. When app create tray icon before Waybar finish launching it is not shown.
Create a script like autostart.sh, start waybar there, then do like 5 second delay and start apps that has tray icons.
this post was submitted on 30 Apr 2024
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or just slap a "sleep 5 &&" in front of the command in your hyprland config. e.g. "exec-once= sleep 5 && qbittorrent"